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<p>A compact representation of the gapping pattern for one sequence in an alignment.  
 <a href="classmoltk_1_1EString.html#details">More...</a></p>

<p><code>#include &lt;<a class="el" href="EString_8hpp_source.html">EString.hpp</a>&gt;</code></p>
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Collaboration diagram for moltk::EString:</div>
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<p><a href="classmoltk_1_1EString-members.html">List of all members.</a></p>
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Classes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1EString_1_1const__iterator.html">const_iterator</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Iterator for accessing the residue positions encoded in an estring.  <a href="classmoltk_1_1EString_1_1const__iterator.html#details">More...</a><br/></td></tr>
<tr><td colspan="2"><h2><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1EString.html#ad5c5f1ca824e409441a132595727516a">EString</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1EString.html">EString</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1EString.html#ae5141544f2f35fd6e7dc52e433cf840d">operator*</a> (const <a class="el" href="classmoltk_1_1EString.html">EString</a> &amp;rhs) const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1EString.html">EString</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1EString.html#aef861c7800f5665af4af9eab4a791795">append_run</a> (int run)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1EString.html">EString</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1EString.html#aeb89cc399d87b5ebe50ee41bae4024bd">operator&lt;&lt;</a> (int run)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1EString.html#abccf52caeb356f6ed7e9f34aaa14c7e3">ungapped_length</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1EString.html#a7c4543e6d5c1a7d467bd91f4b22e95a3">total_length</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1EString_1_1const__iterator.html">const_iterator</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1EString.html#ab86a2dae75151c1e8bd542e052c7b6ff">begin</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1EString_1_1const__iterator.html">const_iterator</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1EString.html#abfc1fa93f66f077a932107cc3faabaf9">end</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1EString.html#a586773d72e57fe5a86ecaf3ae61aeabc">reverse</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1EString.html#a805c088cf32ad2fb4ab0ad28b10e876c">operator==</a> (const <a class="el" href="classmoltk_1_1EString.html">EString</a> &amp;rhs) const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1EString.html#a3cc39e881687891eed0af5fa1e33d90c">operator!=</a> (const <a class="el" href="classmoltk_1_1EString.html">EString</a> &amp;rhs) const </td></tr>
<tr><td colspan="2"><h2><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::vector&lt; int &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1EString.html#a3569a7942663b16e4294bcd5ddbb25cc">runs</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1EString.html#af930d7290e6b6a0be911a194069c2cfa">m_ungapped_length</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1EString.html#a2900d588fd81ac22258b3039dc367a62">m_total_length</a></td></tr>
<tr><td colspan="2"><h2><a name="friends"></a>
Friends</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::ostream &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1EString.html#ae4f1df70ed9a50bfbd573defd2c90d49">operator&lt;&lt;</a> (std::ostream &amp;os, const <a class="el" href="classmoltk_1_1EString.html">EString</a> &amp;e)</td></tr>
</table>
<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><p>A compact representation of the gapping pattern for one sequence in an alignment. </p>
</div><hr/><h2>Constructor &amp; Destructor Documentation</h2>
<a class="anchor" id="ad5c5f1ca824e409441a132595727516a"></a><!-- doxytag: member="moltk::EString::EString" ref="ad5c5f1ca824e409441a132595727516a" args="()" -->
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<hr/><h2>Member Function Documentation</h2>
<a class="anchor" id="aef861c7800f5665af4af9eab4a791795"></a><!-- doxytag: member="moltk::EString::append_run" ref="aef861c7800f5665af4af9eab4a791795" args="(int run)" -->
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<a class="anchor" id="ab86a2dae75151c1e8bd542e052c7b6ff"></a><!-- doxytag: member="moltk::EString::begin" ref="ab86a2dae75151c1e8bd542e052c7b6ff" args="() const " -->
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<a class="anchor" id="a3cc39e881687891eed0af5fa1e33d90c"></a><!-- doxytag: member="moltk::EString::operator!=" ref="a3cc39e881687891eed0af5fa1e33d90c" args="(const EString &amp;rhs) const " -->
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<a class="anchor" id="ae5141544f2f35fd6e7dc52e433cf840d"></a><!-- doxytag: member="moltk::EString::operator*" ref="ae5141544f2f35fd6e7dc52e433cf840d" args="(const EString &amp;rhs) const " -->
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          <td class="memname"><a class="el" href="classmoltk_1_1EString.html">EString</a> moltk::EString::operator* </td>
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<a class="anchor" id="a805c088cf32ad2fb4ab0ad28b10e876c"></a><!-- doxytag: member="moltk::EString::operator==" ref="a805c088cf32ad2fb4ab0ad28b10e876c" args="(const EString &amp;rhs) const " -->
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<a class="anchor" id="a586773d72e57fe5a86ecaf3ae61aeabc"></a><!-- doxytag: member="moltk::EString::reverse" ref="a586773d72e57fe5a86ecaf3ae61aeabc" args="()" -->
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<a class="anchor" id="a7c4543e6d5c1a7d467bd91f4b22e95a3"></a><!-- doxytag: member="moltk::EString::total_length" ref="a7c4543e6d5c1a7d467bd91f4b22e95a3" args="() const " -->
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<a class="anchor" id="abccf52caeb356f6ed7e9f34aaa14c7e3"></a><!-- doxytag: member="moltk::EString::ungapped_length" ref="abccf52caeb356f6ed7e9f34aaa14c7e3" args="() const " -->
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<hr/><h2>Friends And Related Function Documentation</h2>
<a class="anchor" id="ae4f1df70ed9a50bfbd573defd2c90d49"></a><!-- doxytag: member="moltk::EString::operator&lt;&lt;" ref="ae4f1df70ed9a50bfbd573defd2c90d49" args="(std::ostream &amp;os, const EString &amp;e)" -->
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          <td class="paramkey"></td>
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          <td>)</td>
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<hr/><h2>Member Data Documentation</h2>
<a class="anchor" id="a2900d588fd81ac22258b3039dc367a62"></a><!-- doxytag: member="moltk::EString::m_total_length" ref="a2900d588fd81ac22258b3039dc367a62" args="" -->
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          <td class="memname">size_t <a class="el" href="classmoltk_1_1EString.html#a2900d588fd81ac22258b3039dc367a62">moltk::EString::m_total_length</a><code> [protected]</code></td>
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<a class="anchor" id="af930d7290e6b6a0be911a194069c2cfa"></a><!-- doxytag: member="moltk::EString::m_ungapped_length" ref="af930d7290e6b6a0be911a194069c2cfa" args="" -->
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          <td class="memname">size_t <a class="el" href="classmoltk_1_1EString.html#af930d7290e6b6a0be911a194069c2cfa">moltk::EString::m_ungapped_length</a><code> [protected]</code></td>
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<a class="anchor" id="a3569a7942663b16e4294bcd5ddbb25cc"></a><!-- doxytag: member="moltk::EString::runs" ref="a3569a7942663b16e4294bcd5ddbb25cc" args="" -->
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<hr/>The documentation for this class was generated from the following file:<ul>
<li>moltk/<a class="el" href="EString_8hpp_source.html">EString.hpp</a></li>
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